Note: Tax4Fun2 is available unofficially, open source at: https://github.com/ZihaoShu/Tax4Fun2
This plugin was partially built using a modified version of that package.
The plugin takes a TXT file of tab-delimited keyword-value pairs:
fasta: FASTA file of OTU representative sequences. otutable: Tab-delimited OTU table (OTUs are rows, samples are columns) pathtoreference: Path to Tax4Fun2 reference database (you'll need to install this using the above URL)
The plugin outputs both functional and pathway prediction TXT files in the user-specified output directory.